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#34456 - 10/03/14 01:11 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
If I keep the water, I get the same result:
SR2 0 0
SS2 0 0
SX2 0 0
SY2 0 0

What is to be done?

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#34457 - 10/03/14 03:57 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8389
Loc: 39 03 48 N, 77 06 54 W
Find the clues in your output file.
_________________________
Rick Venable
computational chemist


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#34458 - 10/03/14 04:41 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
OK, now for the final part, in the output file I get:

ORREL> ! use final mantime to set AVER, FLUC for output
CORREL> open write unit 1 card name cd@{C}.txt
Parameter: C -> "2"
At line 145 of file /home/themis/c39a2/source/util/parse.src (unit = 5, file = 'test.inp')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::cd2.txt::
OPNLGU> Unit 1 opened for WRITE access to cd2.txt

I think this is the clue, but how do I interpret it?

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#34459 - 10/03/14 09:22 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8389
Loc: 39 03 48 N, 77 06 54 W
The Fortran runtime error message suggests some kind of problem with the file named test.inp; perhaps that file has become corrupted in some way. You have not provided enough information to say any more.
_________________________
Rick Venable
computational chemist


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#34460 - 10/04/14 10:45 AM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
Here is the file test.inp, for 274 POPC lipids.(I made it following the example above, with a saved trajectory file for lipids without water and a psf file written in charm format.The number of atoms in trajectory file match those in psf ):

! the axial avg order parameter for an input C no. @C
! modified for C=C case; first file @FF last file @LF
! subdir @S


! Read initial data files
open unit 1 read form name top_all36_lipid.rtf
read rtf card unit 1
close unit 1
open unit 1 read form name par_all36_lipid.prm
read param card unit 1
close unit 1

! Read parameter file in command line

open read card unit 1 name popc.psf
read psf card unit 1
open read card unit 1 name popc.crd
read coor card unit 1

! number of lipids
set nl = 274
! number of files
calc n = 1

calc mxa @NL * 6 * 4
calc mxs 10 + @NL*2 * 4
calc mxt 2000 * @N

! unsaturation check; beta chain
set ub = 0
define unsat sele atom A 1 C2@C .and. chem CEL1 end
if ub lt ?NSEL set ub ?NSEL
! unsaturation check; gamma chain
set ug = 0
define unsat sele atom A 1 C3@C .and. chem CEL1 end
if ug lt ?NSEL set ug ?NSEL

correl maxtim @MXT maxa @MXA maxs @MXS
enter sr zero
if ub eq 0 enter ss dupl sr
enter sx dupl sr
if ug eq 0 enter sy dupl sr
set k 1
label elp
if ub eq 0 then
enter w@K vect z A @K H@{C}R A @K C2@C
enter a@K vect r A @K H@{C}R A @K C2@C
enter x@K vect z A @K H@{C}S A @K C2@C
enter b@K vect r A @K H@{C}S A @K C2@C
else
enter w@K vect z A @K H@{C}1 A @K C2@C
enter a@K vect r A @K H@{C}1 A @K C2@C
endif
if c gt 15 goto eskip
if ug eq 0 then
enter y@K vect z A @K H@{C}X A @K C3@C
enter c@K vect r A @K H@{C}X A @K C3@C
enter z@K vect z A @K H@{C}Y A @K C3@C
enter d@K vect r A @K H@{C}Y A @K C3@C
else
enter y@K vect z A @K H@{C}1 A @K C3@C
enter c@K vect r A @K H@{C}1 A @K C3@C
endif
label eskip
incr k by 1
if k le @NL goto elp

! OPEN FILES, FILL SERIES VIA TRAJ

open read unit 1 file name popclipidsnowater.dcd

! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM
set k 1
label clp
mantim w@K ratio a@K
mantim w@K squa
mantim w@K mult 1.5
mantim w@K shift -0.5
mantim sr add w@K
if ub eq 0 then
mantim x@K ratio b@K
mantim x@K squa
mantim x@K mult 1.5
mantim x@K shift -0.5
mantim ss add x@K
endif
if c gt 15 goto mskip
mantim y@K ratio c@K
mantim y@K squa
mantim y@K mult 1.5
mantim y@K shift -0.5
mantim sx add y@K
if ug eq 0 then
mantim z@K ratio d@K
mantim z@K squa
mantim z@K mult 1.5
mantim z@K shift -0.5
mantim sy add z@K
endif
label mskip
incr k by 1
if k le @NL goto clp

! use final mantime to set AVER, FLUC for output
open write unit 1 card name cd@{C}.txt
echu 1
mantim sr divi @NL
echo sr@C ?AVER ?FLUC
if ub eq 0 then
mantim ss divi @NL
echo ss@C ?AVER ?FLUC
endif
if c gt 15 goto oskip
mantim sx divi @NL
echo sx@C ?AVER ?FLUC
if ug eq 0 then
mantim sy divi @NL
echo sy@C ?AVER ?FLUC
endif
label oskip
close unit 1

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#34462 - 10/04/14 02:19 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8389
Loc: 39 03 48 N, 77 06 54 W
I don't see any problems with the input; however, the error message suggests there are non-printing control characters present in the file. While one possibility for that is accidental file corruption, sometimes this can occur for files which have been edited on a Windows or Mac OS X machine and then transferred to a Linux machine to run CHARMM. Note that TAB characters are not allowed in CHARMM input scripts. You may need to consult with a local computer guru to help you with this.

One thing you can try is to make a new file by using a graphic cut-and-paste from the old file to a new file, using a text editor on the Linux system. In principle, this should not copy any non-printing characters which may be causing trouble.
_________________________
Rick Venable
computational chemist


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#34463 - 10/04/14 05:42 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
OK, I fixed that error, but I still have results 0.
Here is a sample of the output:

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec FSHIft VATOm VFSWIt
BYGRoup NOEXtnd NOEWald
CUTNB = 14.000 CTEXNB =999.000 CTONNB = 10.000 CTOFNB = 12.000
CGONNB = 0.000 CGOFNB = 10.000
WMIN = 1.500 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 0 atom exclusions.
There are 0 group pairs and 0 group exclusions.
with mode 5 found 106586 exclusions and 97544 interactions(1-4)
found 24112 group exclusions.
Generating nonbond list with Exclusion mode = 5
== PRIMARY == SPACE FOR 10550403 ATOM PAIRS AND 0 GROUP PAIRS
== PRIMARY == SPACE FOR 15825624 ATOM PAIRS AND 0 GROUP PAIRS

General atom nonbond list generation found:
15104476 ATOM PAIRS WERE FOUND FOR ATOM LIST
823754 GROUP PAIRS REQUIRED ATOM SEARCHES


CORREL> enter sr zero

CORREL> if ub eq 0 enter ss dupl sr
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> enter sx dupl sr

CORREL> if ug eq 0 enter sy dupl sr
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL>

CORREL> set k 1
Parameter: K <- "1"

CORREL> label elp

CORREL> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> enter w@K vect z A @K H@{C}R A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter a@K vect r A @K H@{C}R A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter x@K vect z A @K H@{C}S A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> enter b@K vect r A @K H@{C}S A @K C2@C
Parameter: K -> "1"
Parameter: K -> "1"
Parameter: C -> "2"
Parameter: K -> "1"
Parameter: C -> "2"

CORREL> else
Skip commands until next ENDIF

CORREL> if c gt 15 goto eskip





CORREL> ! LOOP OVER LIPIDS; NORM, CALC SCD, ACCUM
CORREL> set k 1
Parameter: K <- "1"

CORREL> label clp

CORREL> mantim w@K ratio a@K ! DIVIDE VECTOR Z BY R (z OF UNIT VECTOR)
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K squa ! z**2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K mult 1.5 ! * 3/2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim w@K shift -0.5 ! - 1/2
Parameter: K -> "1"
NSER: 1
NAMES: W1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sr add w@K
Parameter: K -> "1"
NSER: 1
NAMES: SR
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim x@K ratio b@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K squa
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim x@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: X1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim ss add x@K
Parameter: K -> "1"
NSER: 1
NAMES: SS
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> endif

CORREL> if c gt 15 goto mskip
Comparing "2" and "15".
IF test evaluated as false. Skipping command

CORREL> mantim y@K ratio c@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K squa
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim y@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: Y1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sx add y@K
Parameter: K -> "1"
NSER: 1
NAMES: SX
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> if ug eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim z@K ratio d@K
Parameter: K -> "1"
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K squa
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K mult 1.5
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim z@K shift -0.5
Parameter: K -> "1"
NSER: 1
NAMES: Z1
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: VECT
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 3
VALUE: 0.000000

CORREL> mantim sy add z@K
Parameter: K -> "1"
NSER: 1
NAMES: SY
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> endif

CORREL> label mskip

CORREL> incr k by 1
Parameter: K <- "2"

CORREL> if k le @NL goto clp
Parameter: NL -> "274"
Comparing "2" and "274".
IF test evaluated as true. Performing command



CORREL> ! use final mantime to set AVER, FLUC for output
CORREL> open write unit 1 card name cd@{C}.txt
Parameter: C -> "2"
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::cd2.txt::
OPNLGU> Unit 1 opened for WRITE access to cd2.txt

CORREL> echu 1

CORREL> mantim sr divi @NL
Parameter: NL -> "274"
NSER: 1
NAMES: SR
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> echo sr@C ?AVER ?FLUC
Parameter: C -> "2"
RDCMND substituted energy or value "?AVER" to "0"
RDCMND substituted energy or value "?FLUC" to "0"

CORREL> if ub eq 0 then
Comparing "0" and "0".
IF test evaluated as true. Performing command

CORREL> mantim ss divi @NL
Parameter: NL -> "274"
NSER: 1
NAMES: SS
TOTALS: 0
AVERAGE: 0.000000
FLUCT: 0.000000
VECCOD: 1
CLASS: ZERO
VELCOD: 0
SKIP: 1
DELTA: 0.000000
OFFST: 0.000000
GECOD: 1
VALUE: 0.000000

CORREL> echo ss@C ?AVER ?FLUC
Parameter: C -> "2"
RDCMND substituted energy or value "?AVER" to "0"
RDCMND substituted energy or value "?FLUC" to "0"

CORREL> endif

CORREL> if c gt 15 goto oskip

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#34464 - 10/04/14 05:42 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
Why do I keep getting 0 results?

SR2 0 0
SS2 0 0
SX2 0 0
SY2 0 0

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#34465 - 10/04/14 09:49 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
rmv Offline

Forum Member

Registered: 09/17/03
Posts: 8389
Loc: 39 03 48 N, 77 06 54 W
Please review the READ BEFORE POSTING guidelines for suggestions on the best way to post output logs.

It looks like you may have omitted the all-important TRAJ command, which actually reads the trajectory file(s) and fills the requested time series with data. The comments in the sample inputs are usually important, such as this one:

! OPEN FILES, FILL SERIES VIA TRAJ
_________________________
Rick Venable
computational chemist


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#34466 - 10/05/14 02:12 PM Re: lipid C-D order parameters using CORREL [Re: rmv]
Mih Offline
Forum Member

Registered: 02/10/13
Posts: 25
I didn't ommit. In the script I listed above I included TRAJ command as:

! OPEN FILES, FILL SERIES VIA TRAJ
open read unit 1 file name popclipidsnowater.dcd

I have one file only, popclipidsnowater.dcd. What else should I include?

Also, in the output, I got no errors in opening the trajectory file:
CORREL> ! OPEN FILES, FILL SERIES VIA TRAJ
CORREL> open read unit 1 file name popclipidsnowater.dcd
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 1 with status "KEEP"
VOPEN> Attempting to open::popclipidsnowater.dcd::
OPNLGU> Unit 1 opened for READONLY access to popclipidsnowater.dcd

CORREL>


Thank you,

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